SEPTIN5

Summary

SEPTIN5 (septin 5, HGNC:9164) is a protein-coding gene on chromosome 22q11.21, encoding Septin-5 (Q99719). Filament-forming cytoskeletal GTPase.

This gene is a member of the septin gene family of nucleotide binding proteins, originally described in yeast as cell division cycle regulatory proteins. Septins are highly conserved in yeast, Drosophila, and mouse and appear to regulate cytoskeletal organization. Disruption of septin function disturbs cytokinesis and results in large multinucleate or polyploid cells. This gene is mapped to 22q11, the region frequently deleted in DiGeorge and velocardiofacial syndromes. A translocation involving the MLL gene and this gene has also been reported in patients with acute myeloid leukemia. Alternative splicing results in multiple transcript variants. The presence of a non-consensus polyA signal (AACAAT) in this gene also results in read-through transcription into the downstream neighboring gene (GP1BB; platelet glycoprotein Ib), whereby larger, non-coding transcripts are produced.

Source: NCBI Gene 5413 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 5 total — 1 pathogenic
• Druggable target: yes
• MANE Select transcript: NM_002688

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9164
Approved symbol	SEPTIN5
Name	septin 5
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Aliases	HCDCREL-1, H5, Septin-5, CDCREL-1
Ensembl gene	ENSG00000184702
Ensembl biotype	protein_coding
OMIM	602724
Entrez	5413

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000383045, ENST00000395109, ENST00000406172, ENST00000406395, ENST00000412544, ENST00000413258, ENST00000431124, ENST00000438754, ENST00000455784, ENST00000470814, ENST00000477238, ENST00000480423, ENST00000490204, ENST00000942371

RefSeq mRNA: 2 — MANE Select: NM_002688 NM_001009939, NM_002688

CCDS: CCDS13764, CCDS56224

Canonical transcript exons

ENST00000455784 — 12 exons

Exon	Start	End
ENSE00001717340	19714781	19714791
ENSE00001719277	19714503	19714631
ENSE00003467523	19722428	19723319
ENSE00003815622	19720768	19720869
ENSE00003820014	19720549	19720666
ENSE00003820174	19721822	19721957
ENSE00003820766	19719602	19719698
ENSE00003825366	19722237	19722339
ENSE00003826843	19719806	19719892
ENSE00003826856	19721640	19721736
ENSE00003828129	19720115	19720238
ENSE00003828163	19720320	19720454

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 99.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.3733 / max 533.7153, expressed in 1493 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
191056	18.6700	1120
191054	5.7568	1105
191055	2.8911	853
191051	0.2803	146
191052	0.2585	90
191059	0.1872	93
191053	0.1458	60
191058	0.0991	49
209385	0.0623	27
191057	0.0223	13

Top tissues by expression

267 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right frontal lobe	UBERON:0002810	99.44	gold quality
cortical plate	UBERON:0005343	99.41	gold quality
anterior cingulate cortex	UBERON:0009835	99.17	gold quality
cingulate cortex	UBERON:0003027	99.06	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.98	gold quality
cerebellar hemisphere	UBERON:0002245	98.62	gold quality
cerebellar cortex	UBERON:0002129	98.57	gold quality
ganglionic eminence	UBERON:0004023	98.55	gold quality
apex of heart	UBERON:0002098	98.35	gold quality
right atrium auricular region	UBERON:0006631	98.14	gold quality
prefrontal cortex	UBERON:0000451	98.04	gold quality
nucleus accumbens	UBERON:0001882	97.63	gold quality
amygdala	UBERON:0001876	97.14	gold quality
skin of leg	UBERON:0001511	97.03	gold quality
caudate nucleus	UBERON:0001873	96.98	gold quality
cerebellum	UBERON:0002037	96.72	gold quality
putamen	UBERON:0001874	96.14	gold quality
skin of abdomen	UBERON:0001416	96.00	gold quality
ventricular zone	UBERON:0003053	95.92	gold quality
adenohypophysis	UBERON:0002196	95.67	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.60	gold quality
cardiac atrium	UBERON:0002081	95.58	gold quality
lower esophagus mucosa	UBERON:0035834	95.49	gold quality
right uterine tube	UBERON:0001302	95.02	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.92	gold quality
heart left ventricle	UBERON:0002084	94.89	gold quality
pancreatic ductal cell	CL:0002079	94.69	gold quality
neocortex	UBERON:0001950	94.52	gold quality
ectocervix	UBERON:0012249	94.35	gold quality
pituitary gland	UBERON:0000007	94.12	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-55	yes	222.98
E-MTAB-10042	yes	141.32
E-CURD-122	yes	21.68
E-ANND-3	no	1.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SEPTIN5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-4763-5P	98.75	63.89	854
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-654-3P	98.38	67.61	905
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-5589-5P	98.34	64.82	1148
HSA-MIR-637	97.91	64.05	1517
HSA-MIR-8089	97.74	66.21	1698
HSA-MIR-4667-5P	97.61	66.67	1683
HSA-MIR-6787-5P	97.54	63.85	457
HSA-MIR-1226-3P	97.51	66.32	1063
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-1178-5P	95.83	64.12	504

Literature-anchored findings (GeneRIF, showing 7)

• CDCrel-1 overexpression exerts dopamine-dependent neurotoxicity and may contribute to the development of autosomal-recessive juvenile parkinsonism (PMID:14530399)
• We studied the assembly of three human septins, SEPT4, SEPT5 and SEPT8, with each other (heterotypic) and with themselves (homotypic) using a yeast two-hybrid system. (PMID:15214843)
• the high expression levels of PNUTL1 in human pancreatic endocrine cells that suggests a similar role of this protein in islet cells to that demonstrated in neuronal tissues, and warrants further functional studies of this protein. (PMID:16179808)
• Our finding suggests a role for members of the septin family in the development of proliferative retinal membranes. (PMID:17625225)
• HSP70 and constitutively active HSF1 mediate protection against CDCrel-1-mediated toxicity (PMID:18398426)
• The expression levels of miR-185, SEPT5, LRRK2, and PARK2 genes were measured at a mRNA level in dopaminergic areas of rats’ brains and SHSY-5Y cells using the SYBR Green Real-Time PCR Method. (PMID:31814881)
• Presynaptic Vesicle Protein SEPTIN5 Regulates the Degradation of APP C-Terminal Fragments and the Levels of Abeta. (PMID:33203136)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	septin5a	ENSDARG00000013843
danio_rerio	septin5b	ENSDARG00000036031
mus_musculus	Septin5	ENSMUSG00000072214
rattus_norvegicus	Septin5	ENSRNOG00000029912
drosophila_melanogaster	Septin2	FBGN0014029
caenorhabditis_elegans		WBGENE00006795

Paralogs (12): SEPTIN3 (ENSG00000100167), SEPTIN7 (ENSG00000122545), SEPTIN6 (ENSG00000125354), SEPTIN11 (ENSG00000138758), SEPTIN12 (ENSG00000140623), SEPTIN14 (ENSG00000154997), SEPTIN8 (ENSG00000164402), SEPTIN2 (ENSG00000168385), SEPTIN1 (ENSG00000180096), SEPTIN9 (ENSG00000184640), SEPTIN10 (ENSG00000186522), TMEM250 (ENSG00000238227)

Protein

Protein identifiers

Septin-5 — Q99719 (reviewed: Q99719)

Alternative names: Cell division control-related protein 1, Peanut-like protein 1

All UniProt accessions (9): Q99719, C9JM82, E7EPG2, E7EQM7, E7EX32, F8W9E5, G3XAH0, H7C299, X5DNA9

UniProt curated annotations — full annotation on UniProt →

Function. Filament-forming cytoskeletal GTPase. May play a role in cytokinesis (Potential). May play a role in platelet secretion.

Subunit / interactions. Septins polymerize into heterooligomeric protein complexes that form filaments, and can associate with cellular membranes, actin filaments and microtubules. GTPase activity is required for filament formation. Interacts with SEPTIN2 and SEPTIN5. In platelets, associated with a complex containing STX4. Interacts with PRKN; this interaction leads to SEPTIN5 ubiquitination and degradation. Interacts with DYRK1A. Interacts with STX1A; in the cerebellar cortex.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed at high levels in the CNS, as well as in heart and platelets (at protein level).

Post-translational modifications. Phosphorylated by DYRK1A. In platelets, phosphorylated in response to thrombin, phorbol-12-myristate-13-acetate and collagen.

Miscellaneous. In a heterologous system, SEPTIN5 overexpression has been shown to exert dopamine-dependent neurotoxicity. As wild-type PRKN, but not familial-linked PRKN mutants, ubiquitinates mouse SEPTIN5 and promotes its degradation, it has been suggested that a deficiency in SEPTIN5 degradation may contribute to the development of early onset Parkinson disease 2 (PARK2).

Similarity. Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Septin GTPase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q99719-1	1	yes
Q99719-2	2

RefSeq proteins (2): NP_001009939, NP_002679* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016491	Septin	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR030379	G_SEPTIN_dom	Domain

Pfam: PF00735

UniProt features (21 total): binding site 6, modified residue 5, region of interest 3, splice variant 2, chain 1, domain 1, sequence conflict 1, helix 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6WCU	X-RAY DIFFRACTION	1.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99719-F1	77.71	0.20

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (6): 248; 263; 51–58; 85; 111; 190–198

Post-translational modifications (5): 13, 168, 225, 327, 336

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 115 (showing top): GOBP_BEHAVIOR, GOBP_VESICLE_LOCALIZATION, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_ADULT_BEHAVIOR, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_VESICLE_TARGETING, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, MODULE_66, GOBP_EXOCYTOSIS

GO Biological Process (8): intracellular protein localization (GO:0008104), obsolete synaptic vesicle targeting (GO:0016080), regulation of exocytosis (GO:0017157), adult behavior (GO:0030534), social behavior (GO:0035176), cytoskeleton-dependent cytokinesis (GO:0061640), regulation of synaptic vesicle exocytosis (GO:2000300), cell division (GO:0051301)

GO Molecular Function (7): GTPase activity (GO:0003924), structural molecule activity (GO:0005198), GTP binding (GO:0005525), identical protein binding (GO:0042802), molecular adaptor activity (GO:0060090), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (8): plasma membrane (GO:0005886), septin ring (GO:0005940), synaptic vesicle (GO:0008021), microtubule cytoskeleton (GO:0015630), septin complex (GO:0031105), cell division site (GO:0032153), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
behavior	2
molecular_function	2
binding	2
cytoskeleton	2
cell cortex	2
septin cytoskeleton	2
cellular anatomical structure	2
macromolecule localization	1
exocytosis	1
regulation of vesicle-mediated transport	1
regulation of secretion by cell	1
biological process involved in intraspecies interaction between organisms	1
cytokinesis	1
synaptic vesicle exocytosis	1
regulation of neurotransmitter secretion	1
regulation of regulated secretory pathway	1
cellular process	1
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
protein binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
membrane	1
cell periphery	1
exocytic vesicle	1
presynapse	1
protein-containing complex	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SEPTIN5	SEPTIN4	O43236	937
SEPTIN5	GP1BB	P13224	898
SEPTIN5	GNB1L	Q9BYB4	891
SEPTIN5	SEPTIN11	Q9NVA2	837
SEPTIN5	SEPTIN6	Q14141	804
SEPTIN5	SEPTIN7	Q16181	798
SEPTIN5	SYP	P08247	767
SEPTIN5	TBX1	O43435	751
SEPTIN5	SNAP25	P13795	735
SEPTIN5	SNCAIP	Q9Y6H5	713
SEPTIN5	SEPTIN8	Q92599	705
SEPTIN5	PRODH	O43272	679
SEPTIN5	GSC2	O15499	674
SEPTIN5	GPR37	O15354	663
SEPTIN5	PRODH	O43272	658

IntAct

159 interactions, top by confidence:

A	B	Type	Score
SEPTIN2	SEPTIN6	psi-mi:“MI:0914”(association)	0.950
SEPTIN5	SEPTIN11	psi-mi:“MI:0915”(physical association)	0.910
SEPTIN11	SEPTIN5	psi-mi:“MI:0915”(physical association)	0.910
SEPTIN5	SEPTIN11	psi-mi:“MI:0407”(direct interaction)	0.910
SEPTIN11	SEPTIN5	psi-mi:“MI:2364”(proximity)	0.910
SEPTIN1	SEPTIN5	psi-mi:“MI:0915”(physical association)	0.870
SEPTIN5	SEPTIN6	psi-mi:“MI:0915”(physical association)	0.870
SEPTIN5	SEPTIN1	psi-mi:“MI:0915”(physical association)	0.870
SEPTIN6	SEPTIN5	psi-mi:“MI:0915”(physical association)	0.870
SEPTIN7	SEPTIN6	psi-mi:“MI:0914”(association)	0.850
SEPTIN5	SEPTIN12	psi-mi:“MI:0915”(physical association)	0.830
SEPTIN12	SEPTIN5	psi-mi:“MI:0915”(physical association)	0.830

BioGRID (111): SEPT2 (Two-hybrid), SEPT6 (Two-hybrid), SEPT7 (Two-hybrid), SEPT11 (Two-hybrid), SEPT5 (Two-hybrid), SEPT5 (Two-hybrid), SEPT5 (Two-hybrid), SEPT6 (Two-hybrid), SEPT10 (Two-hybrid), SEPT5 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT10 (Co-fractionation)

ESM2 similar proteins: A0A096MJN4, A2BGU8, A4FUM1, A5D7Q3, A5PJU9, A6QQL3, B0BNF1, B0KWP7, B1H120, B1MTN8, B2KIE9, B3GNI6, B5FW69, O36023, O43236, P28661, P32468, P40797, P42209, P48010, Q08DM7, Q0VC68, Q0VCP4, Q14141, Q2KJB1, Q3SZN0, Q4R4X5, Q4R555, Q4V8G5, Q5EB96, Q5PQK1, Q5R6R7, Q5REG8, Q6AXA6, Q6IRQ5, Q8C1B7, Q8C650, Q8CHH9, Q8IYM1, Q92599

Diamond homologs: A0A096MJN4, A0A3Q0KDV9, A1L0Y5, A2BGU8, A2VE99, A4FUM1, A5D7Q3, A5PJU9, A6QQL3, B0BNF1, B0KWP7, B1H120, B1MTN8, B2KIE9, B3GNI6, B5FW69, G1UB61, O36023, O43236, O55131, O60165, P25342, P28661, P32457, P32458, P32468, P39826, P39827, P40797, P41901, P42207, P42208, P42209, P48008, P48009, P48010, P54359, Q04921, Q08DM7, Q09116

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
PRKN	“down-regulates quantity”	SEPTIN5	ubiquitination
PRKN	“down-regulates quantity by destabilization”	SEPTIN5	polyubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 61 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
cytoskeleton-dependent cytokinesis	12	163.2×	2e-22
intracellular protein localization	14	24.8×	1e-13

Disease & clinical

Clinical variants and AI predictions

ClinVar

5 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	2
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
831644	NC_000022.10:g.(?19163623)(19770565_?)del	Pathogenic

SpliceAI

1689 predictions. Top by Δscore:

Variant	Effect	Δscore
22:19719589:ATCCT:A	acceptor_gain	1.0000
22:19719590:T:G	acceptor_gain	1.0000
22:19719593:T:A	acceptor_gain	1.0000
22:19719600:A:AC	acceptor_loss	1.0000
22:19719600:A:AG	acceptor_gain	1.0000
22:19719600:AG:A	acceptor_gain	1.0000
22:19719601:G:GG	acceptor_gain	1.0000
22:19719601:GG:G	acceptor_gain	1.0000
22:19719601:GGA:G	acceptor_gain	1.0000
22:19719601:GGAC:G	acceptor_gain	1.0000
22:19719601:GGACA:G	acceptor_gain	1.0000
22:19719694:GGCTG:G	donor_gain	1.0000
22:19719695:GCTGG:G	donor_gain	1.0000
22:19719696:CTG:C	donor_gain	1.0000
22:19719696:CTGGT:C	donor_loss	1.0000
22:19719698:GGT:G	donor_loss	1.0000
22:19719699:G:GG	donor_gain	1.0000
22:19719700:T:A	donor_loss	1.0000
22:19719794:A:AG	acceptor_gain	1.0000
22:19719794:ACCT:A	acceptor_gain	1.0000
22:19719795:C:G	acceptor_gain	1.0000
22:19719797:T:TA	acceptor_gain	1.0000
22:19719801:T:TA	acceptor_gain	1.0000
22:19719804:A:AG	acceptor_gain	1.0000
22:19719804:AG:A	acceptor_gain	1.0000
22:19719804:AGGT:A	acceptor_gain	1.0000
22:19719805:G:GT	acceptor_gain	1.0000
22:19719805:GG:G	acceptor_gain	1.0000
22:19719805:GGT:G	acceptor_gain	1.0000
22:19719805:GGTG:G	acceptor_gain	1.0000

AlphaMissense

2475 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:19721929:C:A	R308S	1.000
22:19719623:G:C	G26R	0.999
22:19719626:T:C	F27L	0.999
22:19719627:T:C	F27S	0.999
22:19719628:C:A	F27L	0.999
22:19719628:C:G	F27L	0.999
22:19719653:C:A	R36S	0.999
22:19719654:G:C	R36P	0.999
22:19719667:G:C	K40N	0.999
22:19719667:G:T	K40N	0.999
22:19719674:T:C	F43L	0.999
22:19719676:T:A	F43L	0.999
22:19719676:T:G	F43L	0.999
22:19719820:G:T	G56W	0.999
22:19719821:G:A	G56E	0.999
22:19720181:T:C	L102P	0.999
22:19720187:T:C	L104P	0.999
22:19720391:G:C	R145P	0.999
22:19720405:G:C	D150H	0.999
22:19720412:G:C	R152P	0.999
22:19720422:C:G	C155W	0.999
22:19720600:C:A	N183K	0.999
22:19720600:C:G	N183K	0.999
22:19721659:T:A	V246D	0.999
22:19721707:G:A	G262D	0.999
22:19721721:T:A	W267R	0.999
22:19721721:T:C	W267R	0.999
22:19721724:G:T	G268W	0.999
22:19721891:T:C	L295P	0.999
22:19721921:A:T	E305V	0.999

dbSNP variants (sampled 300 via entrez): RS1000029080 (22:19718335 C>A,T), RS1000060878 (22:19723059 C>G,T), RS1000070980 (22:19722911 T>A,C), RS1000267092 (22:19723150 C>T), RS1000461398 (22:19716998 T>A), RS1000923428 (22:19713878 G>A), RS1001616852 (22:19718662 T>G), RS1001737125 (22:19715431 G>T), RS1001928244 (22:19715097 C>T), RS1001977571 (22:19713604 A>G), RS1002082708 (22:19719966 C>T), RS1002326898 (22:19713861 G>A), RS1003280098 (22:19718403 C>G), RS1003796250 (22:19718851 G>C,T), RS1003923429 (22:19717643 C>T)

Disease associations

OMIM: gene MIM:602724 | disease phenotypes: MIM:188400

GenCC curated gene-disease

Mondo (1): DiGeorge syndrome (MONDO:0008564)

Orphanet (1): 22q11.2 deletion syndrome (Orphanet:567)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST002057_6	DNA methylation (parent-of-origin)	6.000000e-08
GCST004351_11	Bone ultrasound measurement (broadband ultrasound attenuation)	3.000000e-07
GCST004351_2	Bone ultrasound measurement (broadband ultrasound attenuation)	2.000000e-08
GCST004599_219	Mean platelet volume	2.000000e-21
GCST004603_147	Platelet count	1.000000e-12
GCST004616_173	Platelet distribution width	9.000000e-22
GCST005991_50	Platelet count	1.000000e-10
GCST006288_414	Heel bone mineral density	1.000000e-53
GCST006288_692	Heel bone mineral density	6.000000e-104
GCST006288_91	Heel bone mineral density	3.000000e-47
GCST006979_187	Heel bone mineral density	3.000000e-271
GCST006979_188	Heel bone mineral density	5.000000e-15
GCST010732_17	Sensory peripheral neuropathy in microtubule targeting agent-treated breast cancer	8.000000e-06
GCST90002395_615	Mean platelet volume	1.000000e-73
GCST90002401_342	Platelet distribution width	4.000000e-41
GCST90002402_640	Platelet count	5.000000e-30

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0022599	DNA methylation
EFO:0004514	bone quantitative ultrasound measurement
EFO:0004309	platelet count
EFO:0007984	platelet component distribution width
EFO:0009270	heel bone mineral density
EFO:0005260	response to antimicrotubule agent

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004062	DiGeorge Syndrome	C05.660.207.103.500; C14.240.400.021.500; C14.280.400.044.500; C15.604.451.249.500; C16.131.077.019.500; C16.131.240.400.021.500; C16.131.260.019.500; C16.131.482.249.500; C16.131.621.207.103.500; C16.320.180.019.500; C19.642.482.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5465347 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Vehicle Emissions	decreases expression, increases abundance, decreases reaction, increases expression	2
Benzo(a)pyrene	decreases expression, increases expression	2
Smoke	increases abundance, increases expression, decreases expression	2
Particulate Matter	decreases reaction, increases expression, decreases expression, increases abundance	2
FR900359	increases phosphorylation	1
propionaldehyde	increases expression	1
trichostatin A	affects expression, decreases reaction	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Bleomycin	decreases expression	1
Camptothecin	increases expression	1
Carmustine	decreases expression	1
Cisplatin	increases expression, affects cotreatment	1
Dactinomycin	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Nickel	affects expression, decreases reaction	1
Niclosamide	increases expression	1
Rotenone	decreases expression	1
Testosterone	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5338461	Binding	Binding affinity to Septin5 (unknown origin) assessed as fold change in protein upregulation at 200 uM preincubated for 2 hrs followed by pronase addition and measured after 30 mins by coomassie blue staining based SDS-PAGE gel analysis	Structurally Diverse Alkaloids with Anti-Renal-Fibrosis Activity from the Centipede Scolopendra subspinipes mutilans. — J Nat Prod

Clinical trials (associated diseases)

31 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00395538	PHASE3	TERMINATED	Effects of PTH Replacement on Bone in Hypoparathyroidism
NCT00576407	PHASE2	COMPLETED	Thymus Transplantation in DiGeorge Syndrome #668
NCT00576836	PHASE2	COMPLETED	Thymus Transplantation Dose in DiGeorge #932
NCT01821781	PHASE2	ACTIVE_NOT_RECRUITING	Immune Disorder HSCT Protocol
NCT05149898	PHASE2	COMPLETED	Open-Label Study of ZYN002 Administered as a Transdermal Gel to Children and Adolescents With 22q11.2 Deletion Syndrome (INSPIRE)
NCT07284641	PHASE2	RECRUITING	Hematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT00566488	PHASE1	COMPLETED	Parathyroid and Thymus Transplantation in DiGeorge #931
NCT00579709	PHASE1	COMPLETED	Thymus Transplantation With Immunosuppression
NCT00849888	PHASE1	TERMINATED	Serum-Free Thymus Transplantation in DiGeorge Anomaly
NCT02895906	PHASE1	COMPLETED	Safety and Efficacy Study of NFC-1 in Subjects Aged 12-17 Years With 22q11.2DS & Associated Neuropsychiatric Conditions
NCT00579527	PHASE1/PHASE2	COMPLETED	Phase I/II Thymus Transplantation With Immunosuppression #950
NCT00004351	Not specified	COMPLETED	Study of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes
NCT00005102	Not specified	UNKNOWN	Immunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT00105274	Not specified	COMPLETED	Velocardiofacial (VCFS; 22q11.2; DiGeorge) Syndrome Study
NCT00278005	Not specified	TERMINATED	Infection in DiGeorge Following CHD Surgery
NCT00556530	Not specified	RECRUITING	Examining Genetic Factors That Affect the Severity of 22q11.2 Deletion Syndrome
NCT00916955	Not specified	COMPLETED	Genetic Modifiers for 22q11.2 Syndrome
NCT01220531	Not specified	COMPLETED	Thymus Transplantation Safety-Efficacy
NCT01781923	Not specified	COMPLETED	Cognitive Remediation in 22q11DS
NCT02381457	Not specified	COMPLETED	SNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT02430584	Not specified	UNKNOWN	Whole Blood Specimen Collection From Pregnant Subjects
NCT02460328	Not specified	COMPLETED	Resolution of Primary Immune Defect in 22q11.2 Deletion Syndrome
NCT02787486	Not specified	COMPLETED	Expanded Noninvasive Genomic Medical Assessment: The Enigma Study
NCT03284060	Not specified	TERMINATED	Social Cognition Training and Cognitive Remediation
NCT04141540	Not specified	COMPLETED	Molecular Variants Associated With Schizophrenia: Differential Analysis of Monozygotic Twins With Variable Phenotypic 22q11
NCT04373226	Not specified	TERMINATED	Arithmetic Abilities in Children With 22q11.2DS
NCT04639388	Not specified	RECRUITING	Understanding of Psychotic Disorders in Children With 22q11.2DS
NCT04639960	Not specified	TERMINATED	Neuroprotective Effects of Risperdal on Brain and Cognition in 22q11 Deletion Syndrome
NCT04647500	Not specified	COMPLETED	Effects of Methylphenidate on Brain and Cognition in 22q11 Deletion Syndrome
NCT05924347	Not specified	RECRUITING	Early Scoliotic Changes in Children at Increased Risk for Scoliosis Development
NCT07493096	Not specified	RECRUITING	Intensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders